Well, I did it! Here's what I needed to do:
* ditch the Debian version of UAE for E-UAE (http://www.rcdrummond.net/uae/) due to a segfault while installing AmiKit and lack of a JIT compiler
* copy AmigaOS3.9 CD to the hard drive and make appropriate device mapping in UAE
* make sure everything in AmiKit: is executable
* add a line to the startup-sequence to set the pure bit for the CopyReplace program or it won't go resident
After that, it was pretty much plain sailing. AmiKit installed 3.9 and I applied the updates and Boing Bags without trouble.